77 lines
2.4 KiB
Cython
77 lines
2.4 KiB
Cython
#!python
|
|
#cython: boundscheck=False
|
|
#cython: wraparound=False
|
|
#cython: cdivision=True
|
|
|
|
cimport cython
|
|
cimport numpy as np
|
|
from libc.math cimport fabs, sqrt, exp, cos, pow
|
|
|
|
from ._typedefs cimport DTYPE_t, ITYPE_t, DITYPE_t
|
|
from ._typedefs import DTYPE, ITYPE
|
|
|
|
######################################################################
|
|
# Inline distance functions
|
|
#
|
|
# We use these for the default (euclidean) case so that they can be
|
|
# inlined. This leads to faster computation for the most common case
|
|
cdef inline DTYPE_t euclidean_dist(DTYPE_t* x1, DTYPE_t* x2,
|
|
ITYPE_t size) nogil except -1:
|
|
cdef DTYPE_t tmp, d=0
|
|
cdef np.intp_t j
|
|
for j in range(size):
|
|
tmp = x1[j] - x2[j]
|
|
d += tmp * tmp
|
|
return sqrt(d)
|
|
|
|
|
|
cdef inline DTYPE_t euclidean_rdist(DTYPE_t* x1, DTYPE_t* x2,
|
|
ITYPE_t size) nogil except -1:
|
|
cdef DTYPE_t tmp, d=0
|
|
cdef np.intp_t j
|
|
for j in range(size):
|
|
tmp = x1[j] - x2[j]
|
|
d += tmp * tmp
|
|
return d
|
|
|
|
|
|
cdef inline DTYPE_t euclidean_dist_to_rdist(DTYPE_t dist) nogil except -1:
|
|
return dist * dist
|
|
|
|
|
|
cdef inline DTYPE_t euclidean_rdist_to_dist(DTYPE_t dist) nogil except -1:
|
|
return sqrt(dist)
|
|
|
|
|
|
######################################################################
|
|
# DistanceMetric base class
|
|
cdef class DistanceMetric:
|
|
# The following attributes are required for a few of the subclasses.
|
|
# we must define them here so that cython's limited polymorphism will work.
|
|
# Because we don't expect to instantiate a lot of these objects, the
|
|
# extra memory overhead of this setup should not be an issue.
|
|
cdef DTYPE_t p
|
|
#cdef DTYPE_t[::1] vec
|
|
#cdef DTYPE_t[:, ::1] mat
|
|
cdef np.ndarray vec
|
|
cdef np.ndarray mat
|
|
cdef DTYPE_t* vec_ptr
|
|
cdef DTYPE_t* mat_ptr
|
|
cdef ITYPE_t size
|
|
cdef object func
|
|
cdef object kwargs
|
|
|
|
cdef DTYPE_t dist(self, DTYPE_t* x1, DTYPE_t* x2,
|
|
ITYPE_t size) nogil except -1
|
|
|
|
cdef DTYPE_t rdist(self, DTYPE_t* x1, DTYPE_t* x2,
|
|
ITYPE_t size) nogil except -1
|
|
|
|
cdef int pdist(self, DTYPE_t[:, ::1] X, DTYPE_t[:, ::1] D) except -1
|
|
|
|
cdef int cdist(self, DTYPE_t[:, ::1] X, DTYPE_t[:, ::1] Y,
|
|
DTYPE_t[:, ::1] D) except -1
|
|
|
|
cdef DTYPE_t _rdist_to_dist(self, DTYPE_t rdist) nogil except -1
|
|
|
|
cdef DTYPE_t _dist_to_rdist(self, DTYPE_t dist) nogil except -1
|